Several analysis-related settings are available for customization by selecting Analysis | Settings from the menu bar. This brings up the Analysis Settings dialog, which contains tabs for three groups of settings.
Application settings
The Bambe, Barce, and Fitch executables are required for running PDM, HMM, and DSS analysis methods respectively. Under Microsoft Windows systems, these files are pre-compiled and included as part of TOPALi, and will be linked to automatically the first time the application is run. Under other systems (Unix/Linux), these files must be compiled externally, before being linked to from within TOPALi.
Tree generation settings
Three tree generation methods are available, ranging from least accurate (but fast), to most accurate (but slower).
The Force all negative branch lengths to be zero option ensures that no trees can be created that have negative branch lengths. When selected, any trees with negative branches will automatically have those branches set to a length of zero instead.
Auto-Partitioning settings
Note that this option affects the auto-partition option available by selecting Analysis | Auto-Partition Alignment, in addition to defining the setting used when a report auto-partitions an alignment for tree selection.